Re: [gmx-users] Which files does "-cpi -append" need?

[Mark Abraham]

Hi,

One could just avoid using -deffnm and avoid creating problems ;-) Or if
the md_0_1 name reveals that what you want is each piece on its own, and to
have to append manually later, use just -noappend and let mdrun generate
md.part0001.log, energy.part0001.log etc for you.

Mark

On Fri, Jan 19, 2018, 17:56 Justin Lemkul  wrote:

>
>
> On 1/19/18 11:53 AM, ZHANG Cheng wrote:
> > Thank you very much Justin! Sorry I did not realise that.
> >
> >
> > I will need to include an "except md_0_1.edr" in the deletion.
> >
> >
> > But does it correct that I can delete all the log files?
> > md_0_1.e
> > md_0_1.o
> > md_0_1.pe
> > md_0_1.po
> >
>
> Those are output from your cluster and its queuing system. They are
> irrelevant to GROMACS.
>
> -Justin
>
> >
> >
> >
> > -- Original --
> > From:  "ZHANG Cheng";<272699...@qq.com>;
> > Date:  Sat, Jan 20, 2018 00:45 AM
> > To:  "gromacs.org_gmx-users";
> >
> > Subject:  Which files does "-cpi -append" need?
> >
> >
> >
> > Dear Gromacs,
> > I run Gromacs on our cluster, and use this command to continue my run
> from last checkpoint.
> > gmx mdrun -deffnm md_0_1 -cpi -append
> >
> >
> > Each new run will generate four log files:
> > md_0_1.e
> > md_0_1.o
> > md_0_1.pe
> > md_0_1.po
> >
> >
> >
> > Gradually, I have thousands of log files. So I used these commands to
> delete all of them in one go, :
> > rm md_0_1.e*
> > rm md_0_1.o*
> > rm md_0_1.pe*
> > rm md_0_1.po*
> >
> >
> >
> >
> > I thought the checkpoint information is only stored in md_0_1.cpt,
> md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did
> not delete.
> >
> >
> > However, after deleting all the log files, and then started a new run, I
> was told:
> > Fatal error:
> > File appending requested, but 1 of the 4 output files are not present or
> are named differently
> >
> >
> >
> > So it seems that the checkpoint information is also in one of those
> md_0_1.e, md_0_1.o, md_0_1.pe, md_0_1.po
> files?
> >
> >
> > Thank you.
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] Which files does "-cpi -append" need?

[Justin Lemkul]

On 1/19/18 11:53 AM, ZHANG Cheng wrote:

Thank you very much Justin! Sorry I did not realise that.


I will need to include an "except md_0_1.edr" in the deletion.


But does it correct that I can delete all the log files?
md_0_1.e
md_0_1.o
md_0_1.pe
md_0_1.po



Those are output from your cluster and its queuing system. They are 
irrelevant to GROMACS.


-Justin





-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Sat, Jan 20, 2018 00:45 AM
To:  "gromacs.org_gmx-users";

Subject:  Which files does "-cpi -append" need?



Dear Gromacs,
I run Gromacs on our cluster, and use this command to continue my run from last 
checkpoint.
gmx mdrun -deffnm md_0_1 -cpi -append


Each new run will generate four log files:
md_0_1.e
md_0_1.o
md_0_1.pe
md_0_1.po



Gradually, I have thousands of log files. So I used these commands to delete 
all of them in one go, :
rm md_0_1.e*
rm md_0_1.o*
rm md_0_1.pe*
rm md_0_1.po*




I thought the checkpoint information is only stored in md_0_1.cpt, 
md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not 
delete.


However, after deleting all the log files, and then started a new run, I was 
told:
Fatal error:
File appending requested, but 1 of the 4 output files are not present or are 
named differently



So it seems that the checkpoint information is also in one of those md_0_1.e, 
md_0_1.o, md_0_1.pe, md_0_1.po files?


Thank you.


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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Re: [gmx-users] Which files does "-cpi -append" need?

[ZHANG Cheng]

Thank you very much Justin! Sorry I did not realise that.


I will need to include an "except md_0_1.edr" in the deletion.


But does it correct that I can delete all the log files?
md_0_1.e   
md_0_1.o
md_0_1.pe   
md_0_1.po





-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Sat, Jan 20, 2018 00:45 AM
To:  "gromacs.org_gmx-users";

Subject:  Which files does "-cpi -append" need?



Dear Gromacs,
I run Gromacs on our cluster, and use this command to continue my run from last 
checkpoint.
gmx mdrun -deffnm md_0_1 -cpi -append


Each new run will generate four log files:
md_0_1.e   
md_0_1.o
md_0_1.pe   
md_0_1.po



Gradually, I have thousands of log files. So I used these commands to delete 
all of them in one go, :
rm md_0_1.e*
rm md_0_1.o*
rm md_0_1.pe*
rm md_0_1.po*




I thought the checkpoint information is only stored in md_0_1.cpt, 
md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not 
delete.


However, after deleting all the log files, and then started a new run, I was 
told:
Fatal error:
File appending requested, but 1 of the 4 output files are not present or are 
named differently



So it seems that the checkpoint information is also in one of those 
md_0_1.e, md_0_1.o, md_0_1.pe, md_0_1.po files?


Thank you.
-- 
Gromacs Users mailing list

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Re: [gmx-users] Which files does "-cpi -append" need?

[Justin Lemkul]

On 1/19/18 11:45 AM, ZHANG Cheng wrote:

Dear Gromacs,
I run Gromacs on our cluster, and use this command to continue my run from last 
checkpoint.
gmx mdrun -deffnm md_0_1 -cpi -append


Each new run will generate four log files:
md_0_1.e
md_0_1.o
md_0_1.pe
md_0_1.po



Gradually, I have thousands of log files. So I used these commands to delete 
all of them in one go, :
rm md_0_1.e*
rm md_0_1.o*
rm md_0_1.pe*
rm md_0_1.po*




I thought the checkpoint information is only stored in md_0_1.cpt, 
md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not 
delete.


However, after deleting all the log files, and then started a new run, I was 
told:
Fatal error:
File appending requested, but 1 of the 4 output files are not present or are 
named differently



So it seems that the checkpoint information is also in one of those md_0_1.e, 
md_0_1.o, md_0_1.pe, md_0_1.po files?


The checkpoint file specifies all the names of the mdrun output files 
that you're trying to append to. By removing md_0_1.e* you have deleted 
md_0_1.edr, which stores your energy data. mdrun can't append to a file 
that isn't there. I suggest you be more judicious in your shell globbing 
to avoid removing important output.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

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[gmx-users] Which files does "-cpi -append" need?

[ZHANG Cheng]

Dear Gromacs,
I run Gromacs on our cluster, and use this command to continue my run from last 
checkpoint.
gmx mdrun -deffnm md_0_1 -cpi -append


Each new run will generate four log files:
md_0_1.e   
md_0_1.o
md_0_1.pe   
md_0_1.po



Gradually, I have thousands of log files. So I used these commands to delete 
all of them in one go, :
rm md_0_1.e*
rm md_0_1.o*
rm md_0_1.pe*
rm md_0_1.po*




I thought the checkpoint information is only stored in md_0_1.cpt, 
md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not 
delete.


However, after deleting all the log files, and then started a new run, I was 
told:
Fatal error:
File appending requested, but 1 of the 4 output files are not present or are 
named differently



So it seems that the checkpoint information is also in one of those 
md_0_1.e, md_0_1.o, md_0_1.pe, md_0_1.po files?


Thank you.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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